networkTempBetaDiv: TAXONOMIC BETA-DIVERSITY FUNCTION calculates beta diversity...

In CeresBarros/ToolsCB: Ceres's Useful R Functions

TAXONOMIC BETA-DIVERSITY FUNCTION calculates beta diversity as the spp turnover between two networks.

Description

TAXONOMIC BETA-DIVERSITY FUNCTION calculates beta diversity as the spp turnover between two networks.

Usage

networkTempBetaDiv(web1, web2, dietcat, method = "all", mode = "composition")

Arguments

web1	first adjency matrix (species network)
web2	second adjency matrix (species network)
dietcat	diet categories (i.e., lowest trophic level nodes that are ubiquitous across all networks)
method	is the method used to calculate beta diversity in 'composition' mode. Options are Sorensen's ("sorensen") and Simpson's ("simpson") beta-diversity and their nested component ("nested") (see Baselga 2010), the Jaccard dissimilarity index ("jaccard"), a multiplicative decomposition of alpha/gamma diversity (where alpha and gamma are calculated as inverse-Simpson; "decompSimpson"), all options ("all"), or any combination of them. All these options calculate beta-diversity (i.e., turnover) in terms of species composition. Defaults to "all"
mode	can be "decompHills", "pairwiseHills" or "composition". "decompHills" and "pairwiseHills" use the econetworks package to calculate beta-diversity based on species and link composition, either through alpha/gamma decomposition ("decompHills") or by calculating pairwise beta-diversity ("pairwiseHills"). In both cases, diversity is calculated using a Hills numbers approach. "composition" calculates beta-diversity based on species composition only, using one of method.

CeresBarros/ToolsCB documentation built on Aug. 23, 2024, 4:22 p.m.